Examples with DatasetImpl org.globalbioticinteractions.dataset.DatasetImpl used on opensource projects

Example 76 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImporterForZOVERTest method importDataset.

@Test
public void importDataset() throws StudyImporterException {
    List<Map<String, String>> interactions = new ArrayList<>();
    DatasetImporterForZOVER importer = new DatasetImporterForZOVER(null, null);
    importer.setDatabases(Collections.singletonList(DatasetImporterForZOVER.ZOVER_CHIROPTERA));
    importer.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            interactions.add(interaction);
        }
    });
    DatasetImpl dataset = new DatasetImpl("some/namespace", new ResourceService() {

        @Override
        public InputStream retrieve(URI resourceName) throws IOException {
            InputStream is = null;
            if (StringUtils.equals("http://www.mgc.ac.cn/cgi-bin/ZOVER/lineage2json1.pl?type=viruses&host=chiroptera", resourceName.toString())) {
                is = getClass().getResourceAsStream("zover/chiroptera_chopped.json");
            } else if (StringUtils.equals("http://www.mgc.ac.cn/ZOVER/json/chiroptera_viruses_363628.json", resourceName.toString())) {
                is = getClass().getResourceAsStream("zover/chiroptera_viruses_363628.json");
            }
            return is;
        }
    }, URI.create("some:uri")) {
    };
    importer.setDataset(dataset);
    importer.importStudy();
    assertThat(interactions.size(), is(1));
    Map<String, String> interaction = interactions.get(0);
    assertThat(interaction.get(SOURCE_TAXON_NAME), is("Torque teno Tadarida brasiliensis virus"));
    assertThat(interaction.get(SOURCE_TAXON_ID), is("NCBI:1543419"));
    assertThat(interaction.get(TARGET_TAXON_NAME), is("Tadarida brasiliensis"));
    assertThat(interaction.get(TARGET_TAXON_ID), is("NCBI:9438"));
    assertThat(interaction.get(INTERACTION_TYPE_NAME), is("pathogenOf"));
    assertThat(interaction.get(INTERACTION_TYPE_ID), is("http://purl.obolibrary.org/obo/RO_0002556"));
    assertThat(interaction.get(REFERENCE_CITATION), is(nullValue()));
    assertThat(interaction.get(REFERENCE_URL), is("https://www.ncbi.nlm.nih.gov/nuccore/KM434181"));
    assertThat(interaction.get(REFERENCE_DOI), is(nullValue()));
    assertThat(interaction.get(REFERENCE_ID), is("urn:lsid:cn.ac.mgc:tick:363628"));
}

Example 77 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class NodeFactoryWithDatasetContextTest method createStudy.

@Test
public void createStudy() {
    NodeFactory factory = Mockito.mock(NodeFactory.class);
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    NodeFactoryWithDatasetContext factoryWithDS = new NodeFactoryWithDatasetContext(factory, dataset);
    StudyImpl study = new StudyImpl("some title", new DOI("123", "abc"), "some citation");
    study.setExternalId("some:id");
    factoryWithDS.createStudy(study);
    ArgumentCaptor<Study> argument = ArgumentCaptor.forClass(Study.class);
    verify(factory).createStudy(argument.capture());
    assertEquals("some title", argument.getValue().getTitle());
    assertEquals("some citation", argument.getValue().getCitation());
    assertEquals("10.123/abc", argument.getValue().getDOI().toString());
    assertEquals("some:id", argument.getValue().getExternalId());
}

Example 78 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImplTest method useCitationFromMultipleTableDefinitions.

@Test
public void useCitationFromMultipleTableDefinitions() throws IOException {
    Dataset dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    dataset.setConfig(new ObjectMapper().readTree(getClass().getResourceAsStream("/org/eol/globi/data/test-meta-globi-default-external-schemas.json")));
    assertThat(dataset.getCitation(), is("Seltzer, Carrie; Wysocki, William; Palacios, Melissa; Eickhoff, Anna; Pilla, Hannah; Aungst, Jordan; Mercer, Aaron; Quicho, Jamie; Voss, Neil; Xu, Man; J. Ndangalasi, Henry; C. Lovett, Jon; J. Cordeiro, Norbert (2015): Plant-animal interactions from Africa. figshare. https://dx.doi.org/10.6084/m9.figshare.1526128"));
}

Example 79 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetProxyTest method getMappedResource.

@Test
public void getMappedResource() throws IOException, URISyntaxException {
    URL original = getClass().getResource("/org/globalbioticinteractions/content/original.txt");
    URL proxied = getClass().getResource("/org/globalbioticinteractions/content/proxied.txt");
    JsonNode configProxy = new ObjectMapper().readTree("{ \"resources\": { \"archive\": \"" + proxied.toURI() + "\" } }");
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfig(null);
    final String hashOfOriginal = "0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5";
    final String hashOfProxied = "b09f17ea1b5ca77b7a01a3ed62c84b38578817eddb34f827666c898a27504f67";
    DatasetProxy datasetProxy = new DatasetProxy(dataset);
    datasetProxy.setConfig(configProxy);
    DatasetProxy testDataset = datasetProxy;
    TestHashUtil.assertContentHash(testDataset.retrieve(URI.create("archive")), hashOfProxied);
    JsonNode config = new ObjectMapper().readTree("{ \"resources\": { \"archive\": \"" + original.toURI() + "\" } }");
    testDataset = getTestDataset(config, configProxy);
    TestHashUtil.assertContentHash(testDataset.retrieve(URI.create("archive")), hashOfProxied);
    testDataset = getTestDataset(config, null);
    TestHashUtil.assertContentHash(testDataset.retrieve(URI.create("archive")), hashOfOriginal);
}

Example 80 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImportUtilTest method listDependencies.

@Test
public void listDependencies() throws StudyImporterException, IOException {
    String jsonConfig = "{" + "  \"format\": \"dwca\", " + "  \"citation\": \"The MSB Division of Parasitology Collection\"," + "  \"url\": \"http://ipt.vertnet.org:8080/ipt/archive.do?r=msb_para\"," + "  \"references\": [" + "    {" + "      \"format\": \"dwca\"," + "      \"url\": \"http://ipt.vertnet.org:8080/ipt/archive.do?r=msb_host\"," + "      \"citation\": \"The MSB Division of Host Collection\"" + "    }, {" + "      \"format\": \"dwca\"," + "      \"url\": \"http://ipt.vertnet.org:8080/ipt/archive.do?r=msb_host2\"," + "      \"citation\": \"The MSB Division of Host Collection2\"" + "    }]" + "}";
    final DatasetImpl datasetOrig = new DatasetImpl("name/space", URI.create("some:uri"), in -> in);
    JsonNode objectNode = new ObjectMapper().readTree(jsonConfig);
    datasetOrig.setConfig(objectNode);
    final List<Dataset> references = getReferences(datasetOrig);
    assertThat(references.size(), Is.is(2));
}